SAXSdb — 4ezo

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Antibacterial protein PR-39 × 1 （P80054） SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Antibacterial protein PR-39 × 1 （P80054） SULFATE ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Antibacterial protein PR-39 × 2 （P80054） SULFATE ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 389–607 Author chain B； PDBConstruct 1–219； UniProt 389–607

Antibacterial protein PR-39

OrganismNot specified

UniProt P80054

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Chaperone protein DnaK × 1 （P0A6Y8） SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Chaperone protein DnaK × 1 （P0A6Y8） SULFATE ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Chaperone protein DnaK × 2 （P0A6Y8） SULFATE ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PR39_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–15； UniProt 131–145 Author chain D； PDBConstruct 1–15； UniProt 131–145

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ezo
Deposition date deposition_date	2012-05-03
Structure title title	Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39 (residues 1 to 15)
Keywords keywords	chaperone, peptide binding, CHAPERONE-PEPTIDE BINDING PROTEIN complex; CHAPERONE/PEPTIDE BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4ezo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ezo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ezo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.20 Å
Rg (electron density)	20.70 Å
Total Rg	21.55 Å
Atom count	1722
Residues	223
Excluded volume	30407 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ezo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ezo__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ezo__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Chaperone protein DnaK
Molecular weight formula_weight	23820.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3684

VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Antibacterial protein PR-39
Molecular weight formula_weight	1917.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

RRRPRPPYLPRPRPP

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4ezoA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Substrate Binding Domain Of DNAk; Chain A, domain 1

Domain ID domain_id	4ezoA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ezoB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Substrate Binding Domain Of DNAk; Chain A, domain 1

Domain ID domain_id	4ezoB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	77.632 Å
Unit-cell length b length_b	161.268 Å
Unit-cell length c length_c	44.693 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	24.800 Å
R factor r_factor	0.2055
R_work r_work	0.2044
R_free r_free	0.2396

Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39 (residues 1 to 15)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

State in the Current Structure

Other States of the Same Protein in the Database

Antibacterial protein PR-39

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ezo__assembly_1__model_1

4ezo__assembly_1__model_1 | I(q)

4ezo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39 (residues 1 to 15)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Antibacterial protein PR-39

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ezo__assembly_1__model_1

4ezo__assembly_1__model_1 | I(q)

4ezo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)